Eric Banks 6bee6a1b53 Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles. ... Previously, we would strip out the PLs and AD values since they were no longer accurate. However, this is not ideal because then that information is just lost and 1) users complain on the forum and post it as a bug and 2) it gives us problems in both the current and future (single sample) calling pipelines because we subset samples/alleles all the time and lose info. Now the PLs and AD get correctly selected down. While I was in there I also refactored some related code in subsetDiploidAlleles(). There were no real changes there - I just broke it out into smaller chunks as per our best practices. Added unit tests and updated integration tests. Addressed reviews.		2013-12-03 09:23:03 -05:00
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annotator	Improvements to the reference model pipeline.	2013-11-01 17:58:25 -04:00
beagle	Simpler FILTER and info field encoding for BeagleOutputToVCF	2013-06-14 15:56:13 -04:00
bqsr	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -04:00
compression/reducereads	Bug fix for RR: stop (incorrectly) pulling the MQ out of the SAMRecord as a byte instead of an int.	2013-11-27 18:55:03 -05:00
diagnostics	add unit tests	2013-10-04 11:44:07 -04:00
diffengine	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
genotyper	Bug fix for something Guillermo added to UG before he left to support calling indels from reduced reads.	2013-11-27 13:54:39 -05:00
haplotypecaller	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00
indels	Bug fix for something Guillermo added to UG before he left to support calling indels from reduced reads.	2013-11-27 13:54:39 -05:00
phasing	Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records.	2013-08-21 15:46:57 -04:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	adding a check for the UNAVAILABLE case of GenotypeType in CountVariants	2013-08-29 17:27:00 -04:00
variantrecalibration	Various VQSR optimizations in both runtime and accuracy.	2013-11-29 13:04:46 -05:00
variantutils	Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles.	2013-12-03 09:23:03 -05:00